We (well mostly I) are currently thinking about a general Graph (That is in the mathematical sense) structure. Basically you have two pools of points (One for combat and one for utility) to spend on a list of options. These options can (and most do) have requirements. In other words you need to buy certain other options before you can buy them. That's how it becomes a graph instead of a set.
That way we can offer a very flexible advancement system that can also work non linear. For example dual wielding would be a side path in the graph, probably a branch of the pistol branch. The graph would be shared by all characters, but with different start nodes. So having characters share branches is quite easy.
With that we can work with level ups that grant the points or with directly rewarding points.
I'll do some graphical examples later, so they should be up tomorrow.

Edit:
That system would completely replace the skill system. So you would directly buy things like Accuracy increases, Psionic powers, Medicine ranks or equipment permits.

Last edited by Anima_ on Tue Mar 26, 2013 2:55 pm, edited 1 time in total.

I approve the graph system! When Anima first showed it to me I was dubious, then I realized the possibilities...
For those who didn't understand much, think like the unit / research advancement charts present in games like Civilization, see example image below:

I am not sure if the engine will allow it, but a very good feature was that you could set a "goal" and the game would automatically pick all the required previous nodes to reach it. This way for the more lazy players if you know that you want to be able to unlock the "Big Guns" perk at level 30 which allows you to use two bazooka at once, you set it and the game will take care of making the right choices.
All of this optional of course, you can still choose to manually make the choices. But I remember some people (rightfully) complaining for Loren when replaying the game for the 10th time, when they had a big levelup screen with 10 characters to level up

Okay here are as promised a few graphical explanations and examples. They only show how requirements works and what requirements are available. At the moment I don't have an actual mock up for the graph. That should come before long though.
Since the images are too big you probably need to use your browsers view image function in the context menu.

These are the five types of requirements we have at our disposal. The upper example is a fulfilled requirement and the lower an unfulfilled requirement. Green boxes are bought, orange boxes can be bought and red boxes can't be bought.

This is a combined example that shows how the requirements can work together.
One of the graphs has a mistake, do you know which?